bioRxiv preprint doi: https://doi.org/10.1101/2021.02.12.431052; this version posted February 13, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 A nadA mutation confers nicotinic acid auxotrophy in pro-carcinogenic intestinal 2 Escherichia coli NC101 3 Lacey R. Lopez,a Cassandra J. Barlogio,a* Christopher A. Broberg,a• Jeremy Wang,b Janelle C. 4 Arthur,a,c,d# 5 aDepartment of Microbiology and Immunology, The University of North Carolina at Chapel Hill, 6 Chapel Hill, North Carolina, United States of America. 7 bDepartment of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North 8 Carolina, United States of America. 9 cCenter for Gastrointestinal Biology and Disease, The University of North Carolina at Chapel 10 Hill, Chapel Hill, North Carolina, United States of America. 11 dLineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, 12 Chapel Hill, North Carolina, United States of America. 13 Running title: Eliminating E. coli micronutrient constraints 14 *Present address: Locus Biosciences, Inc., Durham, North Carolina, United States of America. 15 •Present address: Department of Chemistry, The University of North Carolina at Chapel Hill, 16 Chapel Hill, North Carolina, United States of America 17 #Address correspondence to Janelle C. Arthur, [email protected] 18 Abstract word count (max 250): 204 words 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.02.12.431052; this version posted February 13, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 19 Importance word count (max 120): 120 words 20 Main text word count (max 5000): 3999 words 21 22 Abstract 23 Inflammatory bowel diseases and inflammation-associated colorectal cancer are linked to blooms 24 of adherent-invasive Escherichia coli (AIEC) in the intestinal microbiota. AIEC are functionally 25 defined by their ability to adhere/invade epithelial cells and survive/replicate within 26 macrophages. Changes in micronutrient availability can alter AIEC physiology and interactions 27 with host cells. Thus, culturing AIEC for mechanistic investigations often involves precise 28 nutrient formulation. We observed that the pro-inflammatory and pro-carcinogenic AIEC strain 29 NC101 failed to grow in minimal media (MM). We hypothesized that NC101 was unable to 30 synthesize a vital micronutrient normally found in the host gut. Through nutrient 31 supplementation studies, we identified that NC101 is a nicotinic acid (NA) auxotroph. NA 32 auxotrophy was not observed in the other non-toxigenic E. coli or AIEC strains we tested. 33 Sequencing revealed NC101 has a missense mutation in nadA, a gene encoding quinolinate 34 synthase A that is important for de novo NAD biosynthesis. Correcting the identified nadA point 35 mutation restored NC101 prototrophy without impacting AIEC function, including motility and 36 AIEC-defining survival in macrophages. Our findings, along with the generation of a 37 prototrophic NC101 strain, will greatly enhance the ability to perform in vitro functional studies 38 that are needed for mechanistic investigations on the role of intestinal E. coli in digestive disease. 39 2 bioRxiv preprint doi: https://doi.org/10.1101/2021.02.12.431052; this version posted February 13, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 40 Importance 41 Inflammatory bowel diseases (IBD) and colorectal cancer (CRC) are significant global health 42 concerns that are influenced by gut resident microbes, like adherent-invasive Escherichia coli 43 (AIEC). Nutrient availability influences specialized metabolite production, AIEC-defining 44 functional attributes, and AIEC:host interactions. NC101 is a pro-inflammatory and pro- 45 carcinogenic AIEC strain commonly used for studies on IBD and CRC. We identified that 46 NC101 growth in vitro requires a micronutrient found in the host gut. By correcting an identified 47 mutation, we generated an NC101 strain that no longer has micronutrient restrictions. Our 48 findings will facilitate future research that necessitates precise nutrient manipulation, enhancing 49 AIEC functional studies and investigations on other auxotrophic intestinal microbiota members. 50 Broadly, this will improve the study of bacterial:host interactions impacting health and disease. 51 52 Introduction 53 Inflammatory bowel diseases (IBD), including Crohn’s disease and ulcerative colitis, are a major 54 global health concern that affects over 3 million adults in the United States alone (1, 2). IBD is a 55 chronic and multifactorial disease that is driven by aberrant immune responses to commensal 56 microbes, genetic susceptibility, and environmental factors (3). IBD patients experience painful, 57 chronic, and relapsing intestinal inflammation that can lead to life-threatening complications, 58 including intestinal fibrosis and colorectal cancer (CRC) (4, 5). Experimental models have 59 demonstrated that IBD and CRC can be driven by the intestinal microbiota and that specific 60 microbes, such as Escherichia coli, are associated with human disease (6, 7). IBD and CRC have 3 bioRxiv preprint doi: https://doi.org/10.1101/2021.02.12.431052; this version posted February 13, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 61 no single etiology and no cure (8, 9). Therefore, understanding the function of disease-associated 62 gut microbes may uncover novel therapeutic options for intestinal diseases, like IBD and CRC. 63 Intestinal microbes influence the onset and progression of IBD and CRC via metabolite 64 production and modulation of mucosal immunity (10–14). E. coli are common inhabitants of the 65 intestinal microbiota (15, 16). Strain level differences can alter the pro-inflammatory or pro- 66 carcinogenic potential of E. coli, partly through changes in small molecule production (12–14, 67 17, 18). A pathovar of E. coli, termed adherent-invasive E. coli (AIEC), are enriched in the gut 68 microbiota of human IBD and CRC patients (19). AIEC exacerbate experimental colitis and 69 promote CRC in a variety of murine models (17, 18, 20–24). There is no genetic definition for 70 AIEC (14, 19, 25). Instead, AIEC are classically defined by their ability to adhere/invade 71 epithelial cells and survive/replicate within macrophages (19, 26). Environmental conditions, 72 including nutrient availability and intestinal inflammation, can alter AIEC behavior and impact 73 intestinal colonization and disease (14, 17, 27–30). Therefore, the ability to precisely manipulate 74 AIEC growth conditions is essential for in vitro studies investigating AIEC behavior and 75 production of pro-inflammatory and pro-carcinogenic molecules. 76 E. coli NC101 is a well-known AIEC strain utilized by numerous investigators to study how 77 intestinal E. coli adapt to and influence the host during IBD and CRC (14, 17, 18, 24, 31–33). 78 NC101 was originally isolated from a specific pathogen free wild-type mouse at North Carolina 79 State University (34). Colonizing wild-type mice with NC101 does not induce intestinal 80 pathology, even during monoassociation studies using gnotobiotic animals (17). However, 81 despite a lack of traditional toxins and virulence factors, NC101 induces antigen-driven intestinal 82 inflammation in genetically-susceptible IBD mouse models (e.g. interleukin 10 deficient mice) 83 (34). Thus, NC101 is considered a pathobiont and a highly relevant model organism for defining 4 bioRxiv preprint doi: https://doi.org/10.1101/2021.02.12.431052; this version posted February 13, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 84 how susceptible individuals may mount inappropriate immune responses to seemingly innocuous 85 intestinal E. coli. 86 NC101 adapts to the inflamed intestinal milieu by modulating expression of its gene repertoire 87 (35, 36). Nutrient availability alters AIEC physiology, persistence in the microbiota, and 88 production of pro-inflammatory and pro-carcinogenic mediators (14, 17, 27–30). 89 Monoassociation studies with gnotobiotic mice have led to the discovery of several AIEC- 90 derived host-influencing molecules (i.e. specialized metabolites) that drive inflammation and 91 tumorigenesis, including yersiniabactin and colibactin (17–19). Like many specialized 92 metabolites, yersiniabactin and colibactin are produced via biosynthetic gene clusters that can be 93 activated by changes in micronutrient availability, notably iron (37, 38). The nature of AIEC- 94 derived specialized metabolites makes them difficult to isolate and study in functional assays. 95 Therefore, the repertoire of AIEC-derived metabolites and their impact on the host has been 96 largely unexplored. 97 Variations in micronutrient availability can impact the virulence and physiology of AIEC (27, 98 28, 39). Therefore, culturing AIEC for mechanistic studies necessitates using a simplified base 99 media that allows for precise nutrient manipulation. During our studies, we observed that 100 modified M9 minimal media (MM) does not sustain NC101